Update: removing biobakery from conda channels resolved the issue of requests.exceptions.HTTPError: 404 Client Error: Not Found for url:
Performed update of metaphlan with mamba.
I installed humann3 using conda (following instruction here humann3 – The Huttenhower Lab).
While running humann, encountered error (unable to download from Dropbox). One suggested solution was to upgrade metaphlan v3.0 to 4.0.6 (Announcing HUMAnN 3.7). Running this command resulted in error (see below). I would appreciate suggestions to resolve this issue. Thanks.
(biobakery3) gurjit@PC21:~$ conda install -c bioconda metaphlan=4.0.6
Collecting package metadata (current_repodata.json): failed
>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/gateways/repodata/__init__.py", line 187, in conda_http_errors
yield
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/gateways/repodata/__init__.py", line 153, in repodata
response.raise_for_status()
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/requests/models.py", line 1021, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://conda.anaconda.org/biobakery/linux-64/current_repodata.json
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/requests/models.py", line 971, in json
return complexjson.loads(self.text, **kwargs)
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/simplejson/__init__.py", line 514, in loads
return _default_decoder.decode(s)
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/simplejson/decoder.py", line 386, in decode
obj, end = self.raw_decode(s)
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/simplejson/decoder.py", line 416, in raw_decode
return self.scan_once(s, idx=_w(s, idx).end())
simplejson.errors.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/exception_handler.py", line 16, in __call__
return func(*args, **kwargs)
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/cli/main.py", line 84, in main_subshell
exit_code = do_call(args, p)
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/cli/conda_argparse.py", line 126, in do_call
return getattr(module, func_name)(args, parser)
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/notices/core.py", line 123, in wrapper
return func(*args, **kwargs)
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/cli/main_install.py", line 22, in execute
install(args, parser, "install")
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/cli/install.py", line 309, in install
unlink_link_transaction = solver.solve_for_transaction(
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 153, in solve_for_transaction
unlink_precs, link_precs = self.solve_for_diff(
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 214, in solve_for_diff
final_precs = self.solve_final_state(
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 357, in solve_final_state
ssc = self._collect_all_metadata(ssc)
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/common/io.py", line 83, in decorated
return f(*args, **kwds)
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 571, in _collect_all_metadata
index, r = self._prepare(prepared_specs)
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/core/solve.py", line 1285, in _prepare
reduced_index = get_reduced_index(
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/core/index.py", line 286, in get_reduced_index
new_records = SubdirData.query_all(
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 157, in query_all
result = tuple(
File "/home/gurjit/anaconda3/lib/python3.9/concurrent/futures/_base.py", line 609, in result_iterator
yield fs.pop().result()
File "/home/gurjit/anaconda3/lib/python3.9/concurrent/futures/_base.py", line 446, in result
return self.__get_result()
File "/home/gurjit/anaconda3/lib/python3.9/concurrent/futures/_base.py", line 391, in __get_result
raise self._exception
File "/home/gurjit/anaconda3/lib/python3.9/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 142, in subdir_query
return tuple(
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 164, in query
self.load()
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 264, in load
_internal_state = self._load()
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 321, in _load
repodata, state = fetcher.fetch_latest_parsed()
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/gateways/repodata/__init__.py", line 757, in fetch_latest_parsed
parsed, state = self.fetch_latest()
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/gateways/repodata/__init__.py", line 879, in fetch_latest
raw_repodata = repo.repodata(cache.state) # type: ignore
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/gateways/repodata/__init__.py", line 153, in repodata
response.raise_for_status()
File "/home/gurjit/anaconda3/lib/python3.9/contextlib.py", line 137, in __exit__
self.gen.throw(typ, value, traceback)
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/gateways/repodata/__init__.py", line 234, in conda_http_errors
raise RepodataIsEmpty(
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/conda/exceptions.py", line 527, in __init__
body = response.json()
File "/home/gurjit/anaconda3/lib/python3.9/site-packages/requests/models.py", line 975, in json
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
$ /home/gurjit/anaconda3/bin/conda install -c bioconda metaphlan=4.0.6
environment variables:
CIO_TEST=
CONDA_DEFAULT_ENV=biobakery3
CONDA_EXE=/home/gurjit/anaconda3/bin/conda
CONDA_PREFIX=/home/gurjit/anaconda3/envs/biobakery3
CONDA_PREFIX_1=/home/gurjit/anaconda3
CONDA_PROMPT_MODIFIER=(biobakery3)
CONDA_PYTHON_EXE=/home/gurjit/anaconda3/bin/python
CONDA_ROOT=/home/gurjit/anaconda3
CONDA_SHLVL=2
CURL_CA_BUNDLE=
LD_PRELOAD=
PATH=/home/gurjit/anaconda3/envs/biobakery3/bin:/home/gurjit/anaconda3/cond
abin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr
/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/WINDOWS/system32:/mnt/
c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/Windows
PowerShell/v1.0:/mnt/c/WINDOWS/System32/OpenSSH:/mnt/c/Program
Files/Calibre2:/mnt/c/Program Files (x86)/Common
Files/Acronis/SnapAPI:/mnt/c/Program Files/dotnet:/Docker/host/bin:/mn
t/c/Users/PC21/AppData/Local/Microsoft/WindowsApps:/snap/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
active environment : biobakery3
active env location : /home/gurjit/anaconda3/envs/biobakery3
shell level : 2
user config file : /home/gurjit/.condarc
populated config files : /home/gurjit/.condarc
conda version : 23.5.0
conda-build version : 3.21.5
python version : 3.9.16.final.0
virtual packages : __archspec=1=x86_64
__cuda=11.4=0
__glibc=2.31=0
__linux=5.15.90.1=0
__unix=0=0
base environment : /home/gurjit/anaconda3 (writable)
conda av data dir : /home/gurjit/anaconda3/etc/conda
conda av metadata url : None
channel URLs : bioconda/linux-64
bioconda/noarch
Linux 64 :: Anaconda.org
Noarch :: Anaconda.org
conda-forge/linux-64
conda-forge/noarch
main/linux-64
main/noarch
r/linux-64
r/noarch
package cache : /home/gurjit/anaconda3/pkgs
/home/gurjit/.conda/pkgs
envs directories : /home/gurjit/anaconda3/envs
/home/gurjit/.conda/envs
platform : linux-64
user-agent : conda/23.5.0 requests/2.31.0 CPython/3.9.16 Linux/5.15.90.1-microsoft-standard-WSL2 ubuntu/20.04.6 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False
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